Developing PETSc Documentation¶

General Guidelines¶

Good documentation should be like a bonsai tree: alive, on display, frequently tended, and as small as possible (adapted from these best practices).
Wrong, irrelevant, or confusing documentation is worse than no documentation.

Documentation with Sphinx¶

Sphinx is a well-documented and widely-used set of Python-based tools for building documentation. Most content is written using reStructuredText, a simple markup language.

We use Sphinx to coordinate building the documentation for our web page, as well as a PDF of the Users Manual. To create this PDF, you must have a working LaTeX installation.

These slides contain an overview of Sphinx and how we use(d) it, as of October, 2020.

The documentation build with Sphinx involves configuring a minimal build of PETSc and building some of the classic docs.

Building the HTML docs locally¶

We suggest using a Python 3 virtual environment.

> cd $PETSC_DIR
> python3 -m venv petsc-doc-env
> . petsc-doc-env/bin/activate
> pip install -r doc/requirements.txt
> cd doc
> make html  # may take several minutes

Then open _build/html/index.html with your browser.

Notes:

The above assumes that python3 is Python 3.3 or later. Check with python3 --version.
You may need to install a package like python3-venv.

Sphinx Documentation Guidelines¶

Use the .. code-block:: directive instead of the .. code:: directive for any example code that is not included literally using .. literalinclude::. See below for more details on .. literalinclude.
Any invocable command line statements longer than a few words should be in .. code-block:: sections. Any such statements not in code-block statements must be enclosed by double backticks “``”. For example make all is acceptable but
```
> make PETSC_DIR=/my/path/to/petsc PETSC_ARCH=my-petsc-arch all
```
should be in a block.
All code blocks showing invocation of command line must use the “console” block directive. E.g.
```
.. code-block:: console

   > cd $PETSC_DIR/src/snes/interface
   > ./someprog
   output1
   output2
```
The only exception of this is when displaying raw output, i.e. with no preceding commands. Then one may use just the “::” directive to improve visibility E.g.
```
::

   output1
   output2
```
which renders as
```
output1
output2
```
Notice that now “output1” and “output2” are not greyed out as previously.

Any code blocks that show command line invocations must be preceded by the “>” character. E.g.

.. code-block:: console

   > ./configure --some-args
   > make libs
   > make ./ex1
   > ./ex1 --some-args

All environment variables such as $PETSC_DIR or $PATH must be preceded by the “$” character and be enclosed in double backticks “``”. E.g.
```
Lorem ipsum dolor sit ``$PETSC_DIR``, consectetur adipiscing ``$PETSC_ARCH``...
```
When referring to configuration of PETSc, specifically the $PETSC_DIR/configure script in plain text (not code blocks), it should always be lower-case, enclosed in double backticks “``” and not include “./”. E.g.
```
Lorem ipsum dolor sit ``configure``, consectetur adipiscing elit...
```

If using internal section links to to jump to other places within the documentation, use explicit labels and namespace them appropriately. Do not use autosectionlabel extension, and do not use implicit links. E.g.

.. _doc_mydoc:

======================
Start Document Heading
======================

.. _doc_mydoc_internalheadline:

Internal Headline
=================

And in some other file

.. _tut_mytutorial:

======================
Start Tutorial Heading
======================

A link- :ref:`my link name <doc_mydoc_internalheadline>`

Use the literalinclude directive to directly include pieces of source code, as in the following example. Note that an “absolute” path has been used, which means relative to the root for the Sphinx docs (where conf.py is found).
```
.. literalinclude:: /../src/sys/error/err.c
   :start-at: PetscErrorCode PetscError(
   :end-at: PetscFunctionReturn(0)
   :append: }
```
For robustness to changes in the source files, Use :start-at: and related options when possible, noting that you can also use (positive) values of :lines: relative to this. For languages other than C, use the :language: option to appropriately highlight.
We use the sphinxcontrib-bibtex extension to include citations from BibTeX files. You must include .. bibliography:: blocks at the bottom of a page including citations (example). To cite the same reference in more than one page, use this workaround on one of them (example) 1.
See special instructions on Images.
Prefer formatting styles that are easy to modify and maintain. In particular, use of list-table is recommended.
When using external links with inline URLs, prefer to use anonymous hyperlink references with two trailing underscores, e.g.
```
`link text <https://external.org>`__
```
Use restraint in adding new Sphinx extensions, in particular those which aren’t widely-used and well-supported, or those with hidden system dependencies.

Images¶

PETSc’s documentation is tightly coupled to the source code and tests, and is tracked in the primary PETSc Git repository. However, image files are too large to directly track this way (especially because they persist in the integration branches’ histories).

Therefore, we store image files in a separate git repository and clone it when needed. Any new images required must added the currently-used branch of this repository.

Image Guidelines¶

Whenever possible, use SVG files. SVG is a web-friendly vector format and will be automatically converted to PDF using rsvg-convert 2
Avoid large files and large numbers of images.
Do not add movies or other non-image files.

Adding new images¶

Note the URL and currently-used branch (after -b) for the upstream images repository, as used by the documentation build:

	git clone https://gitlab.com/petsc/images.git -b main-1 --depth=1 images

Decide where in doc/images a new image should go. Use the structure of the doc/ tree itself as a guide.
Create a Merge Request to the currently-used branch of the upstream images repository, adding this image 3.
Once this Merge Request is merged, you may make a Merge Request to the primary PETSc repository, relying on the new image(s).

It may be helpful to place working copies of new image(s) in your local doc/images while iterating on documentation; just don’t forget to update the upstream images repository.

Removing, renaming, moving or updating images¶

Do not directly move, rename, or update images in the images repository. Simply add a logically-numbered new version of the image.

If an image is not used in any integration branch (main or release), add it to the the top-level list of files to delete, in the images repository.

Cleaning up the images repository (maintainers only)¶

If the size of the image repository grows too large,

Create a new branch main-X, where X increments the current value
Create a new commit deleting all files in the to-delete list and clearing the list
Reset the new main-X to a single commit with this new, cleaned-up state
Set main-X as the “default” branch on GitLab (or wherever it is hosted).
Update both release and main in the primary PETSc repository to clone this new branch

Building Classic Documentation¶

Some of the documentation is built by a “classic” process as described below.

The documentation tools listed below can be automatically downloaded and installed by configure.

Sowing: a text processing tool developed by Bill Gropp. This produces the PETSc manual pages; see the Sowing documentation and Manual Page Format.
C2html: A text processing package. This generates the HTML versions of all the source code.

Note: Sowing and c2html have additional dependencies like gcc, g++, and flex and do not use compilers specified to PETSc configure. [Windows users please install the corresponding cygwin packages]

> make alldoc LOC=${PETSC_DIR}

To get a quick preview of manual pages from a single source directory (mainly to debug the manual page syntax):

> cd $PETSC_DIR/src/snes/interface
> make LOC=$PETSC_DIR manualpages_buildcite
> browse $PETSC_DIR/docs/manualpages/SNES/SNESCreate.html  # or suitable command to open the HTML page in a browser

Footnotes

1: The extensions’s development branch supports our use case better (:footcite:), which can be investigated if a release is ever made.
2: rsvg-convert is installable with your package manager, e.g., librsvg2-bin on Debian/Ubuntu systems).
3: Maintainers may directly push commits.

PETSc Testing System The Design of PETSc